Plant Circular RNA Database

Detail information of Zm00001d035960_circ_g.5

			
						 General Information
					
						CircRNA Name
						Zm00001d035960_circ_g.5
					
						ID in PlantcircBase
						zma_circ_008929
					
						Alias
						zma_circ_0002485
					
						Organism
						
							Zea mays						
					
						Position
						
							chr6: 62651281-62672025  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d035960						
					
						Parent gene annotation
						
							DNA-directed RNA polymerase III subunit 2
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d035960_circ_g.1 Zm00001d035960_circ_g.2 Zm00001d035960_circ_g.3 Zm00001d035960_circ_g.4 Zm00001d035960_circ_g.6 Zm00001d035960_circ_g.7 Zm00001d035960_circ_g.8 Zm00001d035960_circ_g.9 Zm00001d035960_circ_g.10 Zm00001d035960_circ_g.11 						
					
						Support reads
						NA
					
						Tissues
						leaf, root
					
						Exon boundary  
						
							Yes-Yes							"Exon boundary" shows whether the splicing sites are on the boundary of exons or not. For example, "Yes-No" represents the donor splicing site is on the exon boundary and the accepter is not on the exon boundary.

						Splicing signals  
						
							GT-AG							The splicing signals of the circRNA. For example, "AG-GT" represents that the donor and the accepter splicing signal is "AG" and "GT", respectively.

						Number of exons covered
						Zm00001d035960_T018:31
Zm00001d035960_T009:30
Zm00001d035960_T025:7
Zm00001d035960_T008:25
Zm00001d035960_T005:30
Zm00001d035960_T024:29
Zm00001d035960_T028:16
Zm00001d035960_T006:30
Zm00001d035960_T023:7
Zm00001d035960_T002:29
Zm00001d035960_T004:31
Zm00001d035960_T001:30
Zm00001d035960_T019:30
Zm00001d035960_T003:31
Zm00001d035960_T029:10
Zm00001d035960_T026:23
Zm00001d035960_T021:30
Zm00001d035960_T015:29
Zm00001d035960_T007:30

General Information
CircRNA Name	Zm00001d035960_circ_g.5
ID in PlantcircBase	zma_circ_008929
Alias	zma_circ_0002485
Organism	Zea mays
Position	chr6: 62651281-62672025 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ
Parent gene	Zm00001d035960
Parent gene annotation	DNA-directed RNA polymerase III subunit 2
Parent gene strand	+
Alternative splicing	Zm00001d035960_circ_g.1 Zm00001d035960_circ_g.2 Zm00001d035960_circ_g.3 Zm00001d035960_circ_g.4 Zm00001d035960_circ_g.6 Zm00001d035960_circ_g.7 Zm00001d035960_circ_g.8 Zm00001d035960_circ_g.9 Zm00001d035960_circ_g.10 Zm00001d035960_circ_g.11
Support reads	NA
Tissues	leaf, root
Exon boundary	Yes-Yes "Exon boundary" shows whether the splicing sites are on the boundary of exons or not. For example, "Yes-No" represents the donor splicing site is on the exon boundary and the accepter is not on the exon boundary.
Splicing signals	GT-AG The splicing signals of the circRNA. For example, "AG-GT" represents that the donor and the accepter splicing signal is "AG" and "GT", respectively.
Number of exons covered	Zm00001d035960_T018:31 Zm00001d035960_T009:30 Zm00001d035960_T025:7 Zm00001d035960_T008:25 Zm00001d035960_T005:30 Zm00001d035960_T024:29 Zm00001d035960_T028:16 Zm00001d035960_T006:30 Zm00001d035960_T023:7 Zm00001d035960_T002:29 Zm00001d035960_T004:31 Zm00001d035960_T001:30 Zm00001d035960_T019:30 Zm00001d035960_T003:31 Zm00001d035960_T029:10 Zm00001d035960_T026:23 Zm00001d035960_T021:30 Zm00001d035960_T015:29 Zm00001d035960_T007:30

			
						 Experimental Information
					
						Sanger sequencing for BSS  
						
							NA							Sanger sequencing for back-splicing site (BSS) validation. "Yes" represents Sanger sequencing has been performed to valid the back-splicing site, "No" represents the opposite, "NA" represents "not available".

						PCR primers for BSS   
						
							NA							PCR primers used in back-splicing site (BSS) validation.

						Sanger sequencing for FL   
						
							NA							Sanger sequencing for full-length (FL) sequence validation of circRNAs. "Yes" represents Sanger sequencing has been performed to valid the full-length of circRNA, "No" represents the opposite.

						PCR primers for FL   
						
							NA							 PCR primers used in full-length (FL) sequence validation.

Experimental Information
Sanger sequencing for BSS	NA Sanger sequencing for back-splicing site (BSS) validation. "Yes" represents Sanger sequencing has been performed to valid the back-splicing site, "No" represents the opposite, "NA" represents "not available".
PCR primers for BSS	NA PCR primers used in back-splicing site (BSS) validation.
Sanger sequencing for FL	NA Sanger sequencing for full-length (FL) sequence validation of circRNAs. "Yes" represents Sanger sequencing has been performed to valid the full-length of circRNA, "No" represents the opposite.
PCR primers for FL	NA PCR primers used in full-length (FL) sequence validation.

			
						 Sequences
					
						Splice junction sequence  
						
							CTACAATCACAAACTGAAGACTTCATACTGTTCAATGTGCAAGAATGGGGAAAACATGGCCAAG
ATGAGGCTGCCATACGCTTGCAAGCTTCTATTCCAGgtcattctaattcaagaacagctagcaa
agaatcgtattattgttgacactgatagcaaaggaaggtttgtttaagttatttgattacttca
gaatatac

						Assembled circRNA sequence  
						
							NA
The sequence of a circRNA based on assembly using circseq-cup (Ye et al., 2016) or CIRI-full (Zheng and Zhao, 2018) or CIRCexplorer2 (Zhang et al., 2016).

						Full-length trsnacripts
						
							NA						
					
						Genomic sequence
						
							TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

Sequences
Splice junction sequence	CTACAATCACAAACTGAAGACTTCATACTGTTCAATGTGCAAGAATGGGGAAAACATGGCCAAG ATGAGGCTGCCATACGCTTGCAAGCTTCTATTCCAGgtcattctaattcaagaacagctagcaa agaatcgtattattgttgacactgatagcaaaggaaggtttgtttaagttatttgattacttca gaatatac
Assembled circRNA sequence	NA The sequence of a circRNA based on assembly using circseq-cup (Ye et al., 2016) or CIRI-full (Zheng and Zhao, 2018) or CIRCexplorer2 (Zhang et al., 2016).
Full-length trsnacripts	NA
Genomic sequence	TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.293214357

Conservation Information
Conserved circRNAs	NA
PMCS	0.293214357

			
				
						 Functional Information
					

				
						Coding potential
						Y
					

						Potential coding position
						
							62651504-62651324(+)
62671961-62651324(+)
62651287-62671934(-)
						
					

						Potential amino acid sequence
						
							MDKGKIYLQLNQFNKPIPIIVVMKAMGMESDQETVQMVGRDPRYGDLLFPSIQECASERIYTRQ
RALQYMDEKVTYPGATNQKEGRSYSILRDVFIAHVPVCNGQDTSFWKDQWISDELLSSQLPSLH
SHLLRGVSIEVMSSRLATQLKPHLSRQNHSHCNINLRKKNVLDMNTCDICGLAGEDTNNIIFMC
PFARAFWMRIGVNPNMIAAVQELWTSTAPLGVPMETLSTTLLLGTVWELWKHGDMDYVGNKRFE
LSGQLISLLFELIMQDSITFGLERAISTGNWDIKRFRMHRKGVSQVLSRLSYMASLGYMTRITP
QFEKTRKTSGPRALQPSQWGMLCPCDTPEGEACGLTKNLALLSHVTTDQEEGPLIYLCYSLGVE
DLLSLSSEEIHTPGSFLVMFNGLILGKHKDPQRLVIDLRNLRRSNVIGEFVSIFINEKQLKWFG
HVQRGPSEAPMRSAILRYHSNEKRDRGRPKLTWKEIVKGDLHCVHIASDGGRVCRPLIIADMGI
SRIDETHMEKLRLVCHQHGTCGFDDFLRDGLIEYLDVNEENNALCAMGKQAMGNIAYNQVGYDK
LGAGQNATVAVMGYSGYDIEDAIVMNKSSLDRGFGRCIALKKYTVLKDNYGDGVSDMIVEPQRD
NGVLIKQNMRALDEDGIAGPGQIIRNHDIYVNKRTPKNTSKGIGRALRESDYKDSPALYKGVDG
ETTVVDRVMLCSDTNDKLSIKCIIRHTRRPEVGDKFSSRHGQKGVCGWLTLIFLASRMTIGKMI
ELLGGKAGVSCGRFHYGSAFGEPSGNADKVADISSTLIKHGFSYNGKDFLYSGILGQPLEAYIF
MGPIYYQKLKHMVLDKMHARASGPRVLLTRQPTEGRSRDGGLRLGEMERDCLIAYGASMLIFER
LLLSSDPYQVQKMWLVRLLQSQTEDFILFNVQEWGKHGQDEAAIRLQASIPGHSNSRTASKESY
YC*(+)
MCKNGENMAKMRLPYACKLLFQVILIQEQLAKNRIIVDTDSKGRVIASVTSSTHAIKSKTVIFM
DKGKIYLQLNQFNKPIPIIVVMKAMGMESDQETVQMVGRDPRYGDLLFPSIQECASERIYTRQR
ALQYMDEKVTYPGATNQKEGRSYSILRDVFIAHVPVCNGQDTSFWKDQWISDELLSSQLPSLHS
HLLRGVSIEVMSSRLATQLKPHLSRQNHSHCNINLRKKNVLDMNTCDICGLAGEDTNNIIFMCP
FARAFWMRIGVNPNMIAAVQELWTSTAPLGVPMETLSTTLLLGTVWELWKHGDMDYVGNKRFEL
SGQLISLLFELIMQDSITFGLERAISTGNWDIKRFRMHRKGVSQVLSRLSYMASLGYMTRITPQ
FEKTRKTSGPRALQPSQWGMLCPCDTPEGEACGLTKNLALLSHVTTDQEEGPLIYLCYSLGVED
LLSLSSEEIHTPGSFLVMFNGLILGKHKDPQRLVIDLRNLRRSNVIGEFVSIFINEKQLKWFGH
VQRGPSEAPMRSAILRYHSNEKRDRGRPKLTWKEIVKGDLHCVHIASDGGRVCRPLIIADMGIS
RIDETHMEKLRLVCHQHGTCGFDDFLRDGLIEYLDVNEENNALCAMGKQAMGNIAYNQVGYDKL
GAGQNATVAVMGYSGYDIEDAIVMNKSSLDRGFGRCIALKKYTVLKDNYGDGVSDMIVEPQRDN
GVLIKQNMRALDEDGIAGPGQIIRNHDIYVNKRTPKNTSKGIGRALRESDYKDSPALYKGVDGE
TTVVDRVMLCSDTNDKLSIKCIIRHTRRPEVGDKFSSRHGQKGVCGWLTLIFLASRMTIGKMIE
LLGGKAGVSCGRFHYGSAFGEPSGNADKVADISSTLIKHGFSYNGKDFLYSGILGQPLEAYIFM
GPIYYQKLKHMVLDKMHARASGPRVLLTRQPTEGRSRDGGLRLGEMERDCLIAYGASMLIFERL
LLSSDPYQVQKMWLVRLLQSQTEDFILFNVQEWGKHGQDEAAIRLQASIPGHSNSRTASKESYY
C*(+)
MTWNRSLQAYGSLILAMFSPFLHIEQYEVFSL*(-)
						
					

						Sponge-miRNAs
						
							NA						
					

						circRNA-miRNA-mRNA network
						 VISUALIZATION
					

						Potential function description
						regulating the response to N deficiency
					

			
		

Functional Information
Coding potential	Y
Potential coding position	62651504-62651324(+) 62671961-62651324(+) 62651287-62671934(-)
Potential amino acid sequence	MDKGKIYLQLNQFNKPIPIIVVMKAMGMESDQETVQMVGRDPRYGDLLFPSIQECASERIYTRQ RALQYMDEKVTYPGATNQKEGRSYSILRDVFIAHVPVCNGQDTSFWKDQWISDELLSSQLPSLH SHLLRGVSIEVMSSRLATQLKPHLSRQNHSHCNINLRKKNVLDMNTCDICGLAGEDTNNIIFMC PFARAFWMRIGVNPNMIAAVQELWTSTAPLGVPMETLSTTLLLGTVWELWKHGDMDYVGNKRFE LSGQLISLLFELIMQDSITFGLERAISTGNWDIKRFRMHRKGVSQVLSRLSYMASLGYMTRITP QFEKTRKTSGPRALQPSQWGMLCPCDTPEGEACGLTKNLALLSHVTTDQEEGPLIYLCYSLGVE DLLSLSSEEIHTPGSFLVMFNGLILGKHKDPQRLVIDLRNLRRSNVIGEFVSIFINEKQLKWFG HVQRGPSEAPMRSAILRYHSNEKRDRGRPKLTWKEIVKGDLHCVHIASDGGRVCRPLIIADMGI SRIDETHMEKLRLVCHQHGTCGFDDFLRDGLIEYLDVNEENNALCAMGKQAMGNIAYNQVGYDK LGAGQNATVAVMGYSGYDIEDAIVMNKSSLDRGFGRCIALKKYTVLKDNYGDGVSDMIVEPQRD NGVLIKQNMRALDEDGIAGPGQIIRNHDIYVNKRTPKNTSKGIGRALRESDYKDSPALYKGVDG ETTVVDRVMLCSDTNDKLSIKCIIRHTRRPEVGDKFSSRHGQKGVCGWLTLIFLASRMTIGKMI ELLGGKAGVSCGRFHYGSAFGEPSGNADKVADISSTLIKHGFSYNGKDFLYSGILGQPLEAYIF MGPIYYQKLKHMVLDKMHARASGPRVLLTRQPTEGRSRDGGLRLGEMERDCLIAYGASMLIFER LLLSSDPYQVQKMWLVRLLQSQTEDFILFNVQEWGKHGQDEAAIRLQASIPGHSNSRTASKESY YC(+) MCKNGENMAKMRLPYACKLLFQVILIQEQLAKNRIIVDTDSKGRVIASVTSSTHAIKSKTVIFM DKGKIYLQLNQFNKPIPIIVVMKAMGMESDQETVQMVGRDPRYGDLLFPSIQECASERIYTRQR ALQYMDEKVTYPGATNQKEGRSYSILRDVFIAHVPVCNGQDTSFWKDQWISDELLSSQLPSLHS HLLRGVSIEVMSSRLATQLKPHLSRQNHSHCNINLRKKNVLDMNTCDICGLAGEDTNNIIFMCP FARAFWMRIGVNPNMIAAVQELWTSTAPLGVPMETLSTTLLLGTVWELWKHGDMDYVGNKRFEL SGQLISLLFELIMQDSITFGLERAISTGNWDIKRFRMHRKGVSQVLSRLSYMASLGYMTRITPQ FEKTRKTSGPRALQPSQWGMLCPCDTPEGEACGLTKNLALLSHVTTDQEEGPLIYLCYSLGVED LLSLSSEEIHTPGSFLVMFNGLILGKHKDPQRLVIDLRNLRRSNVIGEFVSIFINEKQLKWFGH VQRGPSEAPMRSAILRYHSNEKRDRGRPKLTWKEIVKGDLHCVHIASDGGRVCRPLIIADMGIS RIDETHMEKLRLVCHQHGTCGFDDFLRDGLIEYLDVNEENNALCAMGKQAMGNIAYNQVGYDKL GAGQNATVAVMGYSGYDIEDAIVMNKSSLDRGFGRCIALKKYTVLKDNYGDGVSDMIVEPQRDN GVLIKQNMRALDEDGIAGPGQIIRNHDIYVNKRTPKNTSKGIGRALRESDYKDSPALYKGVDGE TTVVDRVMLCSDTNDKLSIKCIIRHTRRPEVGDKFSSRHGQKGVCGWLTLIFLASRMTIGKMIE LLGGKAGVSCGRFHYGSAFGEPSGNADKVADISSTLIKHGFSYNGKDFLYSGILGQPLEAYIFM GPIYYQKLKHMVLDKMHARASGPRVLLTRQPTEGRSRDGGLRLGEMERDCLIAYGASMLIFERL LLSSDPYQVQKMWLVRLLQSQTEDFILFNVQEWGKHGQDEAAIRLQASIPGHSNSRTASKESYY C(+) MTWNRSLQAYGSLILAMFSPFLHIEQYEVFSL*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	regulating the response to N deficiency

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d035960_circ_g.5

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